OpenRaiser/Intern-Atlas huggingface dataset:
EndoSurf: Neural Surface Reconstruction of Deformable Tissues with Stereo Endoscope Videos
Venue: arXiv cs.CV 2023
Year: 2023

Reconstructing soft tissues from stereo endoscope videos is an essential prerequisite for many medical applications. Previous methods struggle to produce high-quality geometry and appearance due to their inadequate representations of 3D scenes. To address this issue, we propose a novel neural-field-based method, called EndoSurf, which effectively learns to represent a deforming surface from an RGBD sequence. In EndoSurf, we model surface dynamics, shape, and texture with three neural fields. First, 3D points are transformed from the observed space to the canonical space using the deformation field. The signed distance function (SDF) field and radiance field then predict their SDFs and colors, respectively, with which RGBD images can be synthesized via differentiable volume rendering. We constrain the learned shape by tailoring multiple regularization strategies and disentangling geometry and appearance. Experiments on public endoscope datasets demonstrate that EndoSurf significantly outperforms existing solutions, particularly in reconstructing high-fidelity shapes. Code is available at https://github.com/Ruyi-Zha/endosurf.git.
Chrion: Optimizing Recurrent Neural Network Inference by Collaboratively Utilizing CPUs and GPUs
Venue: arXiv cs.DC 2023
Year: 2023

Deploying deep learning models in cloud clusters provides efficient and prompt inference services to accommodate the widespread application of deep learning. These clusters are usually equipped with host CPUs and accelerators with distinct responsibilities to handle serving requests, i.e. generalpurpose CPUs for input preprocessing and domain-specific GPUs for forward computation. Recurrent neural networks play an essential role in handling temporal inputs and display distinctive computation characteristics because of their high inter-operator parallelism. Hence, we propose Chrion to optimize recurrent neural network inference by collaboratively utilizing CPUs and GPUs. We formulate the model deployment in the CPU-GPU cluster as an NP-hard scheduling problem of directed acyclic graphs on heterogeneous devices. Given an input model in the ONNX format and user-defined SLO requirement, Chrion firstly preprocesses the model by model parsing and profiling, and then partitions the graph to select execution devices for each operator. When an online request arrives, Chrion performs forward computation according to the graph partition by executing the operators on the CPU and GPU in parallel. Our experimental results show that the execution time can be reduced by 19.4% at most in the latency-optimal pattern and GPU memory footprint by 67.5% in the memory-optimal pattern compared with the execution on the GPU.
CohortGPT: An Enhanced GPT for Participant Recruitment in Clinical Study
Venue: arXiv cs.CL 2023
Year: 2023

Participant recruitment based on unstructured medical texts such as clinical notes and radiology reports has been a challenging yet important task for the cohort establishment in clinical research. Recently, Large Language Models (LLMs) such as ChatGPT have achieved tremendous success in various downstream tasks thanks to their promising performance in language understanding, inference, and generation. It is then natural to test their feasibility in solving the cohort recruitment task, which involves the classification of a given paragraph of medical text into disease label(s). However, when applied to knowledge-intensive problem settings such as medical text classification, where the LLMs are expected to understand the decision made by human experts and accurately identify the implied disease labels, the LLMs show a mediocre performance. A possible explanation is that, by only using the medical text, the LLMs neglect to use the rich context of additional information that languages afford. To this end, we propose to use a knowledge graph as auxiliary information to guide the LLMs in making predictions. Moreover, to further boost the LLMs adapt to the problem setting, we apply a chain-of-thought (CoT) sample selection strategy enhanced by reinforcement learning, which selects a set of CoT samples given each individual medical report. Experimental results and various ablation studies show that our few-shot learning method achieves satisfactory performance compared with fine-tuning strategies and gains superb advantages when the available data is limited. The code and sample dataset of the proposed CohortGPT model is available at: https://anonymous.4open.science/r/CohortGPT-4872/
Photo2Relief: Let Human in the Photograph Stand Out
Venue: arXiv cs.CV 2023
Year: 2023

In this paper, we propose a technique for making humans in photographs protrude like reliefs. Unlike previous methods which mostly focus on the face and head, our method aims to generate art works that describe the whole body activity of the character. One challenge is that there is no ground-truth for supervised deep learning. We introduce a sigmoid variant function to manipulate gradients tactfully and train our neural networks by equipping with a loss function defined in gradient domain. The second challenge is that actual photographs often across different light conditions. We used image-based rendering technique to address this challenge and acquire rendering images and depth data under different lighting conditions. To make a clear division of labor in network modules, a two-scale architecture is proposed to create high-quality relief from a single photograph. Extensive experimental results on a variety of scenes show that our method is a highly effective solution for generating digital 2.5D artwork from photographs.
Large Language Model-based System to Provide Immediate Feedback to Students in Flipped Classroom Preparation Learning
Venue: arXiv cs.HC 2023
Year: 2023

This paper proposes a system that uses large language models to provide immediate feedback to students in flipped classroom preparation learning. This study aimed to solve challenges in the flipped classroom model, such as ensuring that students are emotionally engaged and motivated to learn. Students often have questions about the content of lecture videos in the preparation of flipped classrooms, but it is difficult for teachers to answer them immediately. The proposed system was developed using the ChatGPT API on a video-watching support system for preparation learning that is being used in real practice. Answers from ChatGPT often do not align with the context of the student's question. Therefore, this paper also proposes a method to align the answer with the context. This paper also proposes a method to collect the teacher's answers to the students' questions and use them as additional guides for the students. This paper discusses the design and implementation of the proposed system.
Batching for Green AI -- An Exploratory Study on Inference
Venue: arXiv cs.LG 2023
Year: 2023

The batch size is an essential parameter to tune during the development of new neural networks. Amongst other quality indicators, it has a large degree of influence on the model's accuracy, generalisability, training times and parallelisability. This fact is generally known and commonly studied. However, during the application phase of a deep learning model, when the model is utilised by an end-user for inference, we find that there is a disregard for the potential benefits of introducing a batch size. In this study, we examine the effect of input batching on the energy consumption and response times of five fully-trained neural networks for computer vision that were considered state-of-the-art at the time of their publication. The results suggest that batching has a significant effect on both of these metrics. Furthermore, we present a timeline of the energy efficiency and accuracy of neural networks over the past decade. We find that in general, energy consumption rises at a much steeper pace than accuracy and question the necessity of this evolution. Additionally, we highlight one particular network, ShuffleNetV2(2018), that achieved a competitive performance for its time while maintaining a much lower energy consumption. Nevertheless, we highlight that the results are model dependent.
AIGC Empowering Telecom Sector White Paper_chinese
Venue: arXiv cs.AI 2023
Year: 2023

In the global craze of GPT, people have deeply realized that AI, as a transformative technology and key force in economic and social development, will bring great leaps and breakthroughs to the global industry and profoundly influence the future world competition pattern. As the builder and operator of information and communication infrastructure, the telecom sector provides infrastructure support for the development of AI, and even takes the lead in the implementation of AI applications. How to enable the application of AIGC (GPT) and implement AIGC in the telecom sector are questions that telecom practitioners must ponder and answer. Through the study of GPT, a typical representative of AIGC, the authors have analyzed how GPT empowers the telecom sector in the form of scenarios, discussed the gap between the current GPT general model and telecom services, proposed for the first time a Telco Augmented Cognition capability system, provided answers to how to construct a telecom service GPT in the telecom sector, and carried out various practices. Our counterparts in the industry are expected to focus on collaborative innovation around telecom and AI, build an open and shared innovation ecosystem, promote the deep integration of AI and telecom sector, and accelerate the construction of next-generation information infrastructure, in an effort to facilitate the digital transformation of the economy and society.
R2Det: Redemption from Range-view for Accurate 3D Object Detection
Venue: arXiv cs.CV 2023
Year: 2023

LiDAR-based 3D object detection is of paramount importance for autonomous driving. Recent trends show a remarkable improvement for bird's-eye-view (BEV) based and point-based methods as they demonstrate superior performance compared to range-view counterparts. This paper presents an insight that leverages range-view representation to enhance 3D points for accurate 3D object detection. Specifically, we introduce a Redemption from Range-view Module (R2M), a plug-and-play approach for 3D surface texture enhancement from the 2D range view to the 3D point view. R2M comprises BasicBlock for 2D feature extraction, Hierarchical-dilated (HD) Meta Kernel for expanding the 3D receptive field, and Feature Points Redemption (FPR) for recovering 3D surface texture information. R2M can be seamlessly integrated into state-of-the-art LiDAR-based 3D object detectors as preprocessing and achieve appealing improvement, e.g., 1.39%, 1.67%, and 1.97% mAP improvement on easy, moderate, and hard difficulty level of KITTI val set, respectively. Based on R2M, we further propose R2Detector (R2Det) with the Synchronous-Grid RoI Pooling for accurate box refinement. R2Det outperforms existing range-view-based methods by a significant margin on both the KITTI benchmark and the Waymo Open Dataset. Codes will be made publicly available.
Identifying document similarity using a fast estimation of the Levenshtein Distance based on compression and signatures
Venue: arXiv cs.IR 2023
Year: 2023

Identifying document similarity has many applications, e.g., source code analysis or plagiarism detection. However, identifying similarities is not trivial and can be time complex. For instance, the Levenshtein Distance is a common metric to define the similarity between two documents but has quadratic runtime which makes it impractical for large documents where large starts with a few hundred kilobytes. In this paper, we present a novel concept that allows estimating the Levenshtein Distance: the algorithm first compresses documents to signatures (similar to hash values) using a user-defined compression ratio. Signatures can then be compared against each other (some constrains apply) where the outcome is the estimated Levenshtein Distance. Our evaluation shows promising results in terms of runtime efficiency and accuracy. In addition, we introduce a significance score allowing examiners to set a threshold and identify related documents.
Software engineering to sustain a high-performance computing scientific application: QMCPACK
Venue: arXiv cs.SE 2023
Year: 2023

We provide an overview of the software engineering efforts and their impact in QMCPACK, a production-level ab-initio Quantum Monte Carlo open-source code targeting high-performance computing (HPC) systems. Aspects included are: (i) strategic expansion of continuous integration (CI) targeting CPUs, using GitHub Actions runners, and NVIDIA and AMD GPUs in pre-exascale systems, using self-hosted hardware; (ii) incremental reduction of memory leaks using sanitizers, (iii) incorporation of Docker containers for CI and reproducibility, and (iv) refactoring efforts to improve maintainability, testing coverage, and memory lifetime management. We quantify the value of these improvements by providing metrics to illustrate the shift towards a predictive, rather than reactive, sustainable maintenance approach. Our goal, in documenting the impact of these efforts on QMCPACK, is to contribute to the body of knowledge on the importance of research software engineering (RSE) for the sustainability of community HPC codes and scientific discovery at scale.
Model Reporting for Certifiable AI: A Proposal from Merging EU Regulation into AI Development
Venue: arXiv cs.AI 2023
Year: 2023

Despite large progress in Explainable and Safe AI, practitioners suffer from a lack of regulation and standards for AI safety. In this work we merge recent regulation efforts by the European Union and first proposals for AI guidelines with recent trends in research: data and model cards. We propose the use of standardized cards to document AI applications throughout the development process. Our main contribution is the introduction of use-case and operation cards, along with updates for data and model cards to cope with regulatory requirements. We reference both recent research as well as the source of the regulation in our cards and provide references to additional support material and toolboxes whenever possible. The goal is to design cards that help practitioners develop safe AI systems throughout the development process, while enabling efficient third-party auditing of AI applications, being easy to understand, and building trust in the system. Our work incorporates insights from interviews with certification experts as well as developers and individuals working with the developed AI applications.
Towards a TDD maturity model through an anti-patterns framework
Venue: arXiv cs.SE 2023
Year: 2023

Agile software development has been adopted in the industry to quickly react to business change. Since its inception both academia and industry debate the different shades that agile processes and technical practices play in the day-to-day of students and professional developers. Efforts have been made to understand the pros and cons of the Test Driven Development (TDD) practice to develop software as part of a professional environment. Despite the effort of practitioners to list the TDD anti-patterns that unveil undesired effects in the code when practicing TDD, work is needed to understand the causes that lead to that. In that sense, this paper proposes a research project that explores the TDD anti-patterns context and what leads practitioners to face them in the software development context. As a result, we expect to offer a TDD maturity framework to help practitioners in the process of writing code guided by tests and prevent the addition of anti-patterns
Extreme Level Crossing Rate: A New Performance Indicator for URLLC Systems
Venue: arXiv cs.IT 2023
Year: 2023

Level crossing rate (LCR) is a well-known statistical tool that is related to the duration of a random stationary fading process \emph{on average}. In doing so, LCR cannot capture the behavior of \emph{extremely rare} random events. Nonetheless, the latter events play a key role in the performance of ultra-reliable and low-latency communication systems rather than their average (expectation) counterparts. In this paper, for the first time, we extend the notion of LCR to address this issue and sufficiently characterize the statistical behavior of extreme maxima or minima. This new indicator, entitled as extreme LCR (ELCR), is analytically introduced and evaluated by resorting to the extreme value theory and risk assessment. Capitalizing on ELCR, some key performance metrics emerge, i.e., the maximum outage duration, minimum effective duration, maximum packet error rate, and maximum transmission delay. They are all derived in simple closed-form expressions. The theoretical results are cross-compared and verified via extensive simulations whereas some useful engineering insights are manifested.
Consistency-guided Meta-Learning for Bootstrapping Semi-Supervised Medical Image Segmentation
Venue: arXiv cs.CV 2023
Year: 2023

Medical imaging has witnessed remarkable progress but usually requires a large amount of high-quality annotated data which is time-consuming and costly to obtain. To alleviate this burden, semi-supervised learning has garnered attention as a potential solution. In this paper, we present Meta-Learning for Bootstrapping Medical Image Segmentation (MLB-Seg), a novel method for tackling the challenge of semi-supervised medical image segmentation. Specifically, our approach first involves training a segmentation model on a small set of clean labeled images to generate initial labels for unlabeled data. To further optimize this bootstrapping process, we introduce a per-pixel weight mapping system that dynamically assigns weights to both the initialized labels and the model's own predictions. These weights are determined using a meta-process that prioritizes pixels with loss gradient directions closer to those of clean data, which is based on a small set of precisely annotated images. To facilitate the meta-learning process, we additionally introduce a consistency-based Pseudo Label Enhancement (PLE) scheme that improves the quality of the model's own predictions by ensembling predictions from various augmented versions of the same input. In order to improve the quality of the weight maps obtained through multiple augmentations of a single input, we introduce a mean teacher into the PLE scheme. This method helps to reduce noise in the weight maps and stabilize its generation process. Our extensive experimental results on public atrial and prostate segmentation datasets demonstrate that our proposed method achieves state-of-the-art results under semi-supervision. Our code is available at https://github.com/aijinrjinr/MLB-Seg.
Scalable Multi-agent Covering Option Discovery based on Kronecker Graphs
Venue: arXiv cs.LG 2023
Year: 2023

Covering skill (a.k.a., option) discovery has been developed to improve the exploration of RL in single-agent scenarios with sparse reward signals, through connecting the most distant states in the embedding space provided by the Fiedler vector of the state transition graph. Given that joint state space grows exponentially with the number of agents in multi-agent systems, existing researches still relying on single-agent skill discovery either become prohibitive or fail to directly discover joint skills that improve the connectivity of the joint state space. In this paper, we propose multi-agent skill discovery which enables the ease of decomposition. Our key idea is to approximate the joint state space as a Kronecker graph, based on which we can directly estimate its Fiedler vector using the Laplacian spectrum of individual agents' transition graphs. Further, considering that directly computing the Laplacian spectrum is intractable for tasks with infinite-scale state spaces, we further propose a deep learning extension of our method by estimating eigenfunctions through NN-based representation learning techniques. The evaluation on multi-agent tasks built with simulators like Mujoco, shows that the proposed algorithm can successfully identify multi-agent skills, and significantly outperforms the state-of-the-art. Codes are available at: https://github.itap.purdue.edu/Clan-labs/Scalable_MAOD_via_KP.
FEDD -- Fair, Efficient, and Diverse Diffusion-based Lesion Segmentation and Malignancy Classification
Venue: arXiv cs.CV 2023
Year: 2023

Skin diseases affect millions of people worldwide, across all ethnicities. Increasing diagnosis accessibility requires fair and accurate segmentation and classification of dermatology images. However, the scarcity of annotated medical images, especially for rare diseases and underrepresented skin tones, poses a challenge to the development of fair and accurate models. In this study, we introduce a Fair, Efficient, and Diverse Diffusion-based framework for skin lesion segmentation and malignancy classification. FEDD leverages semantically meaningful feature embeddings learned through a denoising diffusion probabilistic backbone and processes them via linear probes to achieve state-of-the-art performance on Diverse Dermatology Images (DDI). We achieve an improvement in intersection over union of 0.18, 0.13, 0.06, and 0.07 while using only 5%, 10%, 15%, and 20% labeled samples, respectively. Additionally, FEDD trained on 10% of DDI demonstrates malignancy classification accuracy of 81%, 14% higher compared to the state-of-the-art. We showcase high efficiency in data-constrained scenarios while providing fair performance for diverse skin tones and rare malignancy conditions. Our newly annotated DDI segmentation masks and training code can be found on https://github.com/hectorcarrion/fedd.
Benchmark datasets for biomedical knowledge graphs with negative statements
Venue: arXiv cs.AI 2023
Year: 2023

Knowledge graphs represent facts about real-world entities. Most of these facts are defined as positive statements. The negative statements are scarce but highly relevant under the open-world assumption. Furthermore, they have been demonstrated to improve the performance of several applications, namely in the biomedical domain. However, no benchmark dataset supports the evaluation of the methods that consider these negative statements. We present a collection of datasets for three relation prediction tasks - protein-protein interaction prediction, gene-disease association prediction and disease prediction - that aim at circumventing the difficulties in building benchmarks for knowledge graphs with negative statements. These datasets include data from two successful biomedical ontologies, Gene Ontology and Human Phenotype Ontology, enriched with negative statements. We also generate knowledge graph embeddings for each dataset with two popular path-based methods and evaluate the performance in each task. The results show that the negative statements can improve the performance of knowledge graph embeddings.